We applied dashr on example ChiP-Seq data (provided by Kevin Luo) - for different histone marks and transcription factor binding examples.
library(plotly)
library(RColorBrewer)
library(dashr)
data1 <- read.table("../data/example_region1/H3K4me3_chip.example_region1.coverage")
data2 <- get(load("../output/H3K4me3_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/H3K4me2_chip.example_region1.coverage")
data2 <- get(load("../output/H3K4me2_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/H3K4me1_chip.example_region1.coverage")
data2 <- get(load("../output/H3K4me1_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/H3K27ac_chip.example_region1.coverage")
data2 <- get(load("../output/H3K27ac_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/H3K36me3_chip.example_region1.coverage")
data2 <- get(load("../output/H3K36me3_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/H3K27me3_chip.example_region1.coverage")
data2 <- get(load("../output/H3K27me3_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
data1 <- read.table("../data/example_region1/CTCF_chip.example_region1.coverage")
data2 <- get(load("../output/CTCF_chip.example_region1.rda"))
table <- data.frame("index" = 1:50000,
"before_smooth" = data1[,5],
"after_smooth" = data2$estimate)
plot_ly(table, x = ~index, name = "default") %>%
add_lines(y = ~before_smooth, alpha = 0.3, line = list(color = 'gray')) %>%
add_lines(y = ~after_smooth, alpha = 1, color = "red") %>%
layout(xaxis = list(title = 'Position on chr5'),
yaxis = list(title = 'read counts (smooth/unsmooth)'))
## Warning in RColorBrewer::brewer.pal(N, "Set2"): minimal value for n is 3, returning requested palette with 3 different levels
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